The first time that I make a joint like this, I cut the first part at the actual/ideal size and cut it free completely, then I cut the joinery for the second part, but leave it fastened in place on the machine, and do a test fit — based on that, I then adjust the file for added clearance, or finish the cut.
I will note that if the parts are not all in the same orientation as will be used when fitting them together that you should calibrate for belt stretch: